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molstar

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A comprehensive macromolecular library.

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/** * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> */ import { BondType } from '../../../mol-model/structure/model/types'; import { SortedArray } from '../../../mol-data/int'; export function typeSymbol(unit, index) { return unit.model.atomicHierarchy.atoms.type_symbol.value(unit.elements[index]); } export function formalCharge(unit, index) { return unit.model.atomicHierarchy.atoms.pdbx_formal_charge.value(unit.elements[index]); } export function atomId(unit, index) { return unit.model.atomicHierarchy.atoms.label_atom_id.value(unit.elements[index]); } export function altLoc(unit, index) { return unit.model.atomicHierarchy.atoms.label_alt_id.value(unit.elements[index]); } export function compId(unit, index) { return unit.model.atomicHierarchy.atoms.label_comp_id.value(unit.elements[index]); } // export function interBondCount(structure, unit, index) { let count = 0; const indices = structure.interUnitBonds.getEdgeIndices(index, unit.id); for (let i = 0, il = indices.length; i < il; ++i) { const b = structure.interUnitBonds.edges[indices[i]]; if (BondType.isCovalent(b.props.flag)) count += 1; } return count; } export function intraBondCount(unit, index) { let count = 0; const { offset, edgeProps: { flags } } = unit.bonds; for (let i = offset[index], il = offset[index + 1]; i < il; ++i) { if (BondType.isCovalent(flags[i])) count += 1; } return count; } export function bondCount(structure, unit, index) { return interBondCount(structure, unit, index) + intraBondCount(unit, index); } export function bondToElementCount(structure, unit, index, element) { let count = 0; eachBondedAtom(structure, unit, index, (unit, index) => { if (typeSymbol(unit, index) === element) count += 1; }); return count; } // export function intraConnectedTo(unit, indexA, indexB) { const { offset, b, edgeProps: { flags } } = unit.bonds; BondType.is; for (let i = offset[indexA], il = offset[indexA + 1]; i < il; ++i) { if (b[i] === indexB && BondType.isCovalent(flags[i])) return true; } return false; } export function interConnectedTo(structure, unitA, indexA, unitB, indexB) { const b = structure.interUnitBonds.getEdge(indexA, unitA.id, indexB, unitB.id); return b && BondType.isCovalent(b.props.flag); } export function connectedTo(structure, unitA, indexA, unitB, indexB) { return unitA === unitB ? intraConnectedTo(unitA, indexA, indexB) : interConnectedTo(structure, unitA, indexA, unitB, indexB); } // export function eachInterBondedAtom(structure, unit, index, cb) { const indices = structure.interUnitBonds.getEdgeIndices(index, unit.id); for (let i = 0, il = indices.length; i < il; ++i) { const b = structure.interUnitBonds.edges[indices[i]]; const uB = structure.unitMap.get(b.unitB); if (BondType.isCovalent(b.props.flag)) cb(uB, b.indexB); } } export function eachIntraBondedAtom(unit, index, cb) { const { offset, b, edgeProps: { flags } } = unit.bonds; for (let i = offset[index], il = offset[index + 1]; i < il; ++i) { if (BondType.isCovalent(flags[i])) cb(unit, b[i]); } } export function eachBondedAtom(structure, unit, index, cb) { eachInterBondedAtom(structure, unit, index, cb); eachIntraBondedAtom(unit, index, cb); } // export function eachResidueAtom(unit, index, cb) { const { offsets } = unit.model.atomicHierarchy.residueAtomSegments; const rI = unit.getResidueIndex(index); for (let i = offsets[rI], il = offsets[rI + 1]; i < il; ++i) { // TODO optimize, avoid search with .indexOf const idx = SortedArray.indexOf(unit.elements, i); if (idx !== -1) cb(idx); } }